Genes controlling virulence phenotypes in Cryptosporidium parasite are unknown, but their identification is needed to guide the development of drugs, to better understand pathogenesis, and to improve the annotation of the genome. The objective of this project is to apply genetic methods to map genes controlling specific phenotypes in C. parvum. In contrast to linkage analysis used in the initial funding period, we propose to apply Linkage Group Selection, a strategy which does not require the cloning of progeny lines derived from experimental crosses. Instead, genetic loci controlling selectable traits are identified by crossing two phenotypically distinct C. parvum lines, exposing uncloned progeny populations to one or multiple rounds of selective pressure, and quantitatively genotyping progeny populations in bulk. Based on phenotypic differences between the parental lines, we will select for early oocyst differentiation, oocyst resistance to bleach, and parasite infectivity to interferon-[unreadable] knock-out mice. During selection, parasites carrying allele(s) conferring the phenotype selected against will be eliminated from the progeny. As a result of meiotic recombination, the proportion of alleles from the sensitive parent will be low in proximity to the locus under selection, creating a "selection valley". Such valleys will be identified by quantitatively genotyping a selected and a control progeny population with a panel of single nucleotide polymorphisms.